Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010705.1 Corchorus olitorius cultivar O-4 contig10737, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35590
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1432 original size:16 final size:16
Alignment explanation
Indices: 1411--1442 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1401 TGTACTAAAG
1411 CTTATATGTTTCAAAC
1 CTTATATGTTTCAAAC
1427 CTTATATGTTTCAAAC
1 CTTATATGTTTCAAAC
1443 TCCTTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
CTTATATGTTTCAAAC
Found at i:8270 original size:27 final size:27
Alignment explanation
Indices: 8231--8284 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
8221 TTTCTACTTC
* **
8231 CGTCTCTTATTATCTGTCGGTTTTCTT
1 CGTCCCTTATTATCTGTCCATTTTCTT
* *
8258 CGTCCCTTTTTATTTGTCCATTTTCTT
1 CGTCCCTTATTATCTGTCCATTTTCTT
8285 TATCACTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.07, C:0.24, G:0.11, T:0.57
Consensus pattern (27 bp):
CGTCCCTTATTATCTGTCCATTTTCTT
Found at i:10130 original size:102 final size:101
Alignment explanation
Indices: 9945--10249 Score: 549
Period size: 102 Copynumber: 3.0 Consensus size: 101
9935 TTTTCAGTGT
* * *
9945 ACTAACAAATTCAATTTTGATGTCGTCTCTTTGCACAGGATTGA-GGTCTTCAGAAAATCACAAA
1 ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGACGGTCGTCAGAAAATCACAAA
10009 ATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
66 ATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
10045 ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGACCGGTCGTCAGAAAATCACAA
1 ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGA-CGGTCGTCAGAAAATCACAA
10110 AATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
65 AATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
10147 ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGACTGGTCGTCAGAAAATCACAA
1 ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGAC-GGTCGTCAGAAAATCACAA
*
10212 AATAAATCCCCACAAATCCTTACTAAGTTGTTAGGGC
65 AATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
10249 A
1 A
10250 AGTAGGGCTC
Statistics
Matches: 198, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
100 42 0.21
101 1 0.01
102 155 0.78
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (101 bp):
ACTAACAAATTCAATTTTGATGTCGCCTCTTTGCACATGATTGACGGTCGTCAGAAAATCACAAA
ATAAATCCCCACAAATCCTTACTAAGTTGCTAGGGC
Found at i:14218 original size:116 final size:116
Alignment explanation
Indices: 14014--14245 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
14004 TAAGTGGAAC
14014 TATCTCATCACCATCATCACCATCCCCACTAGTATCTAAATCAAAATCCTCTTCTTCACTTAAAA
1 TATCTCATCACCATCATCACCATCCCCACTAGTATCTAAATCAAAATCCTCTTCTTCACTTAAAA
14079 GCTCACCATGCTCATTAAAATACATTACCTTCTTGTTAACACAATTTCTAG
66 GCTCACCATGCTCATTAAAATACATTACCTTCTTGTTAACACAATTTCTAG
14130 TATCTCATCACCATCATCACCATCCCCACTAGTATCTAAATCAAAATCCTCTTCTTCACTTAAAA
1 TATCTCATCACCATCATCACCATCCCCACTAGTATCTAAATCAAAATCCTCTTCTTCACTTAAAA
14195 GCTCACCATGCTCATTAAAATACATTACCTTCTTGTTAACACAATTTCTAG
66 GCTCACCATGCTCATTAAAATACATTACCTTCTTGTTAACACAATTTCTAG
14246 CATAGCGACC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (116 bp):
TATCTCATCACCATCATCACCATCCCCACTAGTATCTAAATCAAAATCCTCTTCTTCACTTAAAA
GCTCACCATGCTCATTAAAATACATTACCTTCTTGTTAACACAATTTCTAG
Found at i:14384 original size:23 final size:24
Alignment explanation
Indices: 14358--14403 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14348 GCGCCACCTC
*
14358 CTTC-TCCTTGTATGGAGTTTTCT
1 CTTCTTCCTTGTAAGGAGTTTTCT
*
14381 CTTCTTTCTTGTAAGGAGTTTTC
1 CTTCTTCCTTGTAAGGAGTTTTC
14404 CATGAGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (24 bp):
CTTCTTCCTTGTAAGGAGTTTTCT
Found at i:16188 original size:82 final size:82
Alignment explanation
Indices: 16051--16214 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
16041 ATCTTCTGGG
*
16051 CTTCTTCATGGCTTTTCTTCAATCCTTCGCAATTAAAACTCCAATCTTTAATTCTTGCTTCTTGA
1 CTTCTTCATGGCTTGTCTTCAATCCTTCGCAATTAAAACTCCAATCTTTAATTCTTGCTTCTTGA
16116 AATAATTCTCCAATGAT
66 AATAATTCTCCAATGAT
*
16133 CTTCTTCATGGCTTGTCTTCAATCCTTCGCAATTAAATCTCCAATCTTTAATTCTTGCTTCTTGA
1 CTTCTTCATGGCTTGTCTTCAATCCTTCGCAATTAAAACTCCAATCTTTAATTCTTGCTTCTTGA
*
16198 AATAATTCTTCAATGAT
66 AATAATTCTCCAATGAT
16215 ATTCAAATCT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (82 bp):
CTTCTTCATGGCTTGTCTTCAATCCTTCGCAATTAAAACTCCAATCTTTAATTCTTGCTTCTTGA
AATAATTCTCCAATGAT
Found at i:19672 original size:29 final size:28
Alignment explanation
Indices: 19640--19701 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
19630 TTTAAAAATG
19640 TTTTTAA-AAAATATATAAAAAAACAAAAA
1 TTTTTAAGAAAATA-ATAAAAAAAC-AAAA
* *
19669 TTTTCAAGAAAATAATAAAAAATCAAAA
1 TTTTTAAGAAAATAATAAAAAAACAAAA
19697 TTTTT
1 TTTTT
19702 GTTAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 15 0.52
30 6 0.21
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
TTTTTAAGAAAATAATAAAAAAACAAAA
Found at i:21681 original size:260 final size:260
Alignment explanation
Indices: 21220--21734 Score: 1021
Period size: 260 Copynumber: 2.0 Consensus size: 260
21210 CACTTGCGTA
21220 ACATATCTACCCATAGTACTATTTTTAGCCTTTAGCAACCATATATATGTTCGTATACATAAAGA
1 ACATATCTACCCATAGTACTATTTTTAGCCTTTAGCAACCATATATATGTTCGTATACATAAAGA
*
21285 TGTAATTAGCTATCTTAACAAATAGTATTAAATGTTGAATGTTAGAATATCTCATTGGATTTAAA
66 TGTAATTAGCTATCTTAACAAATAGTATTAAATGTTGAATGTTAGAATATCTCATTCGATTTAAA
21350 AATTAGCTATTAAAAAAGAGTGTCGGAAGCATAGACTGACGTACACGTATAATGGATAACCCATT
131 AATTAGCTATTAAAAAAGAGTGTCGGAAGCATAGACTGACGTACACGTATAATGGATAACCCATT
21415 TTATATTAGATCAGCGGAACTTCCACTTAATTTTAAAGATTTTTTAGAAGAGGCGAGTAACTTCC
196 TTATATTAGATCAGCGGAACTTCCACTTAATTTTAAAGATTTTTTAGAAGAGGCGAGTAACTTCC
21480 ACATATCTACCCATAGTACTATTTTTAGCCTTTAGCAACCATATATATGTTCGTATACATAAAGA
1 ACATATCTACCCATAGTACTATTTTTAGCCTTTAGCAACCATATATATGTTCGTATACATAAAGA
21545 TGTAATTAGCTATCTTAACAAATAGTATTAAATGTTGAATGTTAGAATATCTCATTCGATTTAAA
66 TGTAATTAGCTATCTTAACAAATAGTATTAAATGTTGAATGTTAGAATATCTCATTCGATTTAAA
21610 AATTAGCTATTAAAAAAGAGTGTCGGAAGCATAGACTGACGTACACGTATAATGGATAACCCATT
131 AATTAGCTATTAAAAAAGAGTGTCGGAAGCATAGACTGACGTACACGTATAATGGATAACCCATT
21675 TTATATTAGATCAGCGGAACTTCCACTTAATTTTAAAGATTTTTTAGAAGAGGCGAGTAA
196 TTATATTAGATCAGCGGAACTTCCACTTAATTTTAAAGATTTTTTAGAAGAGGCGAGTAA
21735 TATGGATTAT
Statistics
Matches: 254, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
260 254 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (260 bp):
ACATATCTACCCATAGTACTATTTTTAGCCTTTAGCAACCATATATATGTTCGTATACATAAAGA
TGTAATTAGCTATCTTAACAAATAGTATTAAATGTTGAATGTTAGAATATCTCATTCGATTTAAA
AATTAGCTATTAAAAAAGAGTGTCGGAAGCATAGACTGACGTACACGTATAATGGATAACCCATT
TTATATTAGATCAGCGGAACTTCCACTTAATTTTAAAGATTTTTTAGAAGAGGCGAGTAACTTCC
Found at i:28607 original size:21 final size:22
Alignment explanation
Indices: 28552--28604 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
28542 TTTTATGTGT
* *
28552 TTATAATTCTTATTAATTTGGG
1 TTATAAATCTTATTAATTAGGG
* *
28574 TGATCAA-CTTATTAATTAGGG
1 TTATAAATCTTATTAATTAGGG
28595 TTATAAATCT
1 TTATAAATCT
28605 ATTGCTAGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (22 bp):
TTATAAATCTTATTAATTAGGG
Found at i:33977 original size:21 final size:21
Alignment explanation
Indices: 33951--33996 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33941 TAACAAAGAG
* * *
33951 GGAGATGCTTCCTTCCTCCTA
1 GGAGATGCCTCCTACCTCCCA
33972 GGAGATGCCTCCTACCTCCCA
1 GGAGATGCCTCCTACCTCCCA
33993 GGAG
1 GGAG
33997 GTGTCACCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24
Consensus pattern (21 bp):
GGAGATGCCTCCTACCTCCCA
Done.